Per chromosome imputation report for cohort AdDIT_cohort.
Chromosome index, 23 in total. Skip to the section for a particular chromosome using the buttons below.
Information captured during the processing of this cohort.
| Property | Value |
|---|---|
| FORMAT | MINIMAC2 |
| UPLOADED | 8.4.2021 |
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 12656029 | 73.301 |
| 0.1 | 1220330 | 7.068 |
| 0.2 | 812833 | 4.708 |
| 0.3 | 618189 | 3.580 |
| 0.4 | 497862 | 2.883 |
| 0.5 | 407006 | 2.357 |
| 0.6 | 350434 | 2.030 |
| 0.7 | 291717 | 1.690 |
| 0.8 | 244550 | 1.416 |
| 0.9 | 166949 | 0.967 |
| Total | 17265899 | 100.000 |
Variants binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 751476 | 4.352 |
| 0.4 | 831520 | 4.816 |
| 0.5 | 1066702 | 6.178 |
| 0.6 | 1525605 | 8.836 |
| 0.7 | 2108921 | 12.214 |
| 0.8 | 2793714 | 16.181 |
| 0.9 | 8160726 | 47.265 |
| 1.0 | 27235 | 0.158 |
| Total | 17265899 | 100.000 |
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 966467 | 73.7471 |
| 0.1 | 90429 | 6.9003 |
| 0.2 | 58268 | 4.4462 |
| 0.3 | 45460 | 3.4689 |
| 0.4 | 37556 | 2.8657 |
| 0.5 | 30979 | 2.3639 |
| 0.6 | 26905 | 2.0530 |
| 0.7 | 21703 | 1.6561 |
| 0.8 | 18811 | 1.4354 |
| 0.9 | 13938 | 1.0636 |
| Total | 1310516 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 59290 | 4.5242 |
| 0.4 | 64654 | 4.9335 |
| 0.5 | 82333 | 6.2825 |
| 0.6 | 118554 | 9.0464 |
| 0.7 | 164713 | 12.5686 |
| 0.8 | 211407 | 16.1316 |
| 0.9 | 607677 | 46.3693 |
| 1.0 | 1888 | 0.1441 |
| Total | 1310516 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1062941 | 73.9511 |
| 0.1 | 100912 | 7.0207 |
| 0.2 | 65456 | 4.5539 |
| 0.3 | 49642 | 3.4537 |
| 0.4 | 38704 | 2.6927 |
| 0.5 | 33285 | 2.3157 |
| 0.6 | 28757 | 2.0007 |
| 0.7 | 23484 | 1.6338 |
| 0.8 | 20062 | 1.3958 |
| 0.9 | 14114 | 0.9819 |
| Total | 1437357 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 61380 | 4.2703 |
| 0.4 | 67083 | 4.6671 |
| 0.5 | 86577 | 6.0233 |
| 0.6 | 124233 | 8.6432 |
| 0.7 | 174506 | 12.1408 |
| 0.8 | 234186 | 16.2928 |
| 0.9 | 687424 | 47.8256 |
| 1.0 | 1968 | 0.1369 |
| Total | 1437357 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 891117 | 73.3682 |
| 0.1 | 87680 | 7.2189 |
| 0.2 | 55340 | 4.5563 |
| 0.3 | 42641 | 3.5108 |
| 0.4 | 35907 | 2.9563 |
| 0.5 | 29177 | 2.4022 |
| 0.6 | 24085 | 1.9830 |
| 0.7 | 20728 | 1.7066 |
| 0.8 | 16616 | 1.3680 |
| 0.9 | 11291 | 0.9296 |
| Total | 1214582 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 49880 | 4.1068 |
| 0.4 | 55355 | 4.5575 |
| 0.5 | 70628 | 5.8150 |
| 0.6 | 103762 | 8.5430 |
| 0.7 | 147390 | 12.1350 |
| 0.8 | 193240 | 15.9100 |
| 0.9 | 591545 | 48.7036 |
| 1.0 | 2782 | 0.2290 |
| Total | 1214582 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 880023 | 72.6617 |
| 0.1 | 82339 | 6.7986 |
| 0.2 | 61749 | 5.0985 |
| 0.3 | 44563 | 3.6795 |
| 0.4 | 34021 | 2.8090 |
| 0.5 | 27984 | 2.3106 |
| 0.6 | 24659 | 2.0360 |
| 0.7 | 21830 | 1.8025 |
| 0.8 | 20015 | 1.6526 |
| 0.9 | 13941 | 1.1511 |
| Total | 1211124 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 49972 | 4.1261 |
| 0.4 | 54395 | 4.4913 |
| 0.5 | 70549 | 5.8251 |
| 0.6 | 100328 | 8.2839 |
| 0.7 | 143584 | 11.8554 |
| 0.8 | 193538 | 15.9800 |
| 0.9 | 596919 | 49.2864 |
| 1.0 | 1839 | 0.1518 |
| Total | 1211124 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 809027 | 73.4822 |
| 0.1 | 76612 | 6.9585 |
| 0.2 | 52758 | 4.7919 |
| 0.3 | 40736 | 3.7000 |
| 0.4 | 31654 | 2.8751 |
| 0.5 | 24054 | 2.1848 |
| 0.6 | 22903 | 2.0802 |
| 0.7 | 18065 | 1.6408 |
| 0.8 | 15241 | 1.3843 |
| 0.9 | 9934 | 0.9023 |
| Total | 1100984 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 45191 | 4.1046 |
| 0.4 | 49068 | 4.4567 |
| 0.5 | 62668 | 5.6920 |
| 0.6 | 92455 | 8.3975 |
| 0.7 | 132595 | 12.0433 |
| 0.8 | 178899 | 16.2490 |
| 0.9 | 538678 | 48.9270 |
| 1.0 | 1430 | 0.1299 |
| Total | 1100984 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 789150 | 72.6259 |
| 0.1 | 80092 | 7.3709 |
| 0.2 | 52699 | 4.8499 |
| 0.3 | 40865 | 3.7608 |
| 0.4 | 32870 | 3.0250 |
| 0.5 | 26257 | 2.4164 |
| 0.6 | 22716 | 2.0906 |
| 0.7 | 16932 | 1.5583 |
| 0.8 | 15155 | 1.3947 |
| 0.9 | 9860 | 0.9074 |
| Total | 1086596 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 41971 | 3.8626 |
| 0.4 | 45608 | 4.1973 |
| 0.5 | 58154 | 5.3519 |
| 0.6 | 84972 | 7.8200 |
| 0.7 | 120042 | 11.0475 |
| 0.8 | 164229 | 15.1141 |
| 0.9 | 568019 | 52.2751 |
| 1.0 | 3601 | 0.3314 |
| Total | 1086596 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 709402 | 72.9813 |
| 0.1 | 69801 | 7.1809 |
| 0.2 | 47707 | 4.9080 |
| 0.3 | 35465 | 3.6485 |
| 0.4 | 28955 | 2.9788 |
| 0.5 | 23916 | 2.4604 |
| 0.6 | 18840 | 1.9382 |
| 0.7 | 16489 | 1.6963 |
| 0.8 | 12451 | 1.2809 |
| 0.9 | 9006 | 0.9265 |
| Total | 972032 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 40998 | 4.2178 |
| 0.4 | 45179 | 4.6479 |
| 0.5 | 58368 | 6.0047 |
| 0.6 | 84104 | 8.6524 |
| 0.7 | 118431 | 12.1839 |
| 0.8 | 158943 | 16.3516 |
| 0.9 | 464964 | 47.8342 |
| 1.0 | 1045 | 0.1075 |
| Total | 972032 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 700630 | 73.8905 |
| 0.1 | 64522 | 6.8047 |
| 0.2 | 44128 | 4.6539 |
| 0.3 | 32399 | 3.4169 |
| 0.4 | 27787 | 2.9305 |
| 0.5 | 21621 | 2.2802 |
| 0.6 | 19308 | 2.0363 |
| 0.7 | 15456 | 1.6300 |
| 0.8 | 13494 | 1.4231 |
| 0.9 | 8856 | 0.9340 |
| Total | 948201 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 39596 | 4.1759 |
| 0.4 | 43975 | 4.6377 |
| 0.5 | 55405 | 5.8432 |
| 0.6 | 79921 | 8.4287 |
| 0.7 | 111698 | 11.7800 |
| 0.8 | 151444 | 15.9717 |
| 0.9 | 464502 | 48.9877 |
| 1.0 | 1660 | 0.1751 |
| Total | 948201 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 530147 | 73.3251 |
| 0.1 | 53790 | 7.4397 |
| 0.2 | 34107 | 4.7174 |
| 0.3 | 24677 | 3.4131 |
| 0.4 | 21010 | 2.9059 |
| 0.5 | 15506 | 2.1446 |
| 0.6 | 14614 | 2.0213 |
| 0.7 | 12050 | 1.6666 |
| 0.8 | 9964 | 1.3781 |
| 0.9 | 7144 | 0.9881 |
| Total | 723009 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 29858 | 4.1297 |
| 0.4 | 33239 | 4.5973 |
| 0.5 | 43470 | 6.0124 |
| 0.6 | 62820 | 8.6887 |
| 0.7 | 89398 | 12.3647 |
| 0.8 | 120551 | 16.6735 |
| 0.9 | 342637 | 47.3904 |
| 1.0 | 1036 | 0.1433 |
| Total | 723009 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 611955 | 72.9375 |
| 0.1 | 60678 | 7.2321 |
| 0.2 | 39895 | 4.7550 |
| 0.3 | 28872 | 3.4412 |
| 0.4 | 24833 | 2.9598 |
| 0.5 | 20733 | 2.4711 |
| 0.6 | 16759 | 1.9975 |
| 0.7 | 14541 | 1.7331 |
| 0.8 | 12646 | 1.5072 |
| 0.9 | 8101 | 0.9655 |
| Total | 839013 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 34267 | 4.0842 |
| 0.4 | 38216 | 4.5549 |
| 0.5 | 48690 | 5.8032 |
| 0.6 | 69787 | 8.3177 |
| 0.7 | 98642 | 11.7569 |
| 0.8 | 135065 | 16.0981 |
| 0.9 | 413182 | 49.2462 |
| 1.0 | 1164 | 0.1387 |
| Total | 839013 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 612997 | 73.1761 |
| 0.1 | 58074 | 6.9325 |
| 0.2 | 36815 | 4.3948 |
| 0.3 | 31125 | 3.7155 |
| 0.4 | 23516 | 2.8072 |
| 0.5 | 20691 | 2.4700 |
| 0.6 | 18653 | 2.2267 |
| 0.7 | 14201 | 1.6952 |
| 0.8 | 12440 | 1.4850 |
| 0.9 | 9189 | 1.0969 |
| Total | 837701 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 33534 | 4.0031 |
| 0.4 | 36468 | 4.3533 |
| 0.5 | 46939 | 5.6033 |
| 0.6 | 70533 | 8.4198 |
| 0.7 | 101549 | 12.1223 |
| 0.8 | 135487 | 16.1737 |
| 0.9 | 410930 | 49.0545 |
| 1.0 | 2261 | 0.2699 |
| Total | 837701 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 584684 | 73.1803 |
| 0.1 | 56466 | 7.0674 |
| 0.2 | 36008 | 4.5068 |
| 0.3 | 30383 | 3.8028 |
| 0.4 | 23212 | 2.9053 |
| 0.5 | 18890 | 2.3643 |
| 0.6 | 15974 | 1.9993 |
| 0.7 | 12706 | 1.5903 |
| 0.8 | 12535 | 1.5689 |
| 0.9 | 8106 | 1.0146 |
| Total | 798964 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 33738 | 4.2227 |
| 0.4 | 37108 | 4.6445 |
| 0.5 | 47580 | 5.9552 |
| 0.6 | 68860 | 8.6187 |
| 0.7 | 96242 | 12.0458 |
| 0.8 | 129496 | 16.2080 |
| 0.9 | 384678 | 48.1471 |
| 1.0 | 1262 | 0.1580 |
| Total | 798964 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 437431 | 72.1844 |
| 0.1 | 43121 | 7.1158 |
| 0.2 | 27958 | 4.6136 |
| 0.3 | 22486 | 3.7106 |
| 0.4 | 17350 | 2.8631 |
| 0.5 | 15918 | 2.6268 |
| 0.6 | 12671 | 2.0910 |
| 0.7 | 11187 | 1.8461 |
| 0.8 | 9878 | 1.6301 |
| 0.9 | 7991 | 1.3187 |
| Total | 605991 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 24473 | 4.0385 |
| 0.4 | 26689 | 4.4042 |
| 0.5 | 34626 | 5.7139 |
| 0.6 | 51729 | 8.5363 |
| 0.7 | 74057 | 12.2208 |
| 0.8 | 97783 | 16.1360 |
| 0.9 | 295801 | 48.8128 |
| 1.0 | 833 | 0.1375 |
| Total | 605991 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 398809 | 73.5703 |
| 0.1 | 38977 | 7.1903 |
| 0.2 | 26026 | 4.8011 |
| 0.3 | 18193 | 3.3562 |
| 0.4 | 15213 | 2.8064 |
| 0.5 | 11912 | 2.1975 |
| 0.6 | 10163 | 1.8748 |
| 0.7 | 8998 | 1.6599 |
| 0.8 | 8154 | 1.5042 |
| 0.9 | 5634 | 1.0393 |
| Total | 542079 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 22566 | 4.1629 |
| 0.4 | 25123 | 4.6346 |
| 0.5 | 32842 | 6.0585 |
| 0.6 | 48039 | 8.8620 |
| 0.7 | 65764 | 12.1318 |
| 0.8 | 87489 | 16.1395 |
| 0.9 | 259805 | 47.9275 |
| 1.0 | 451 | 0.0832 |
| Total | 542079 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 346726 | 73.1712 |
| 0.1 | 33035 | 6.9715 |
| 0.2 | 22326 | 4.7116 |
| 0.3 | 16928 | 3.5724 |
| 0.4 | 14676 | 3.0971 |
| 0.5 | 11407 | 2.4073 |
| 0.6 | 9081 | 1.9164 |
| 0.7 | 7902 | 1.6676 |
| 0.8 | 6452 | 1.3616 |
| 0.9 | 5323 | 1.1233 |
| Total | 473856 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 22708 | 4.7922 |
| 0.4 | 26108 | 5.5097 |
| 0.5 | 32786 | 6.9190 |
| 0.6 | 44968 | 9.4898 |
| 0.7 | 59508 | 12.5582 |
| 0.8 | 78155 | 16.4934 |
| 0.9 | 209179 | 44.1440 |
| 1.0 | 444 | 0.0937 |
| Total | 473856 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 391267 | 74.0213 |
| 0.1 | 37989 | 7.1869 |
| 0.2 | 23002 | 4.3516 |
| 0.3 | 18676 | 3.5332 |
| 0.4 | 14486 | 2.7405 |
| 0.5 | 12304 | 2.3277 |
| 0.6 | 10735 | 2.0309 |
| 0.7 | 9284 | 1.7564 |
| 0.8 | 6816 | 1.2895 |
| 0.9 | 4028 | 0.7620 |
| Total | 528587 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 25517 | 4.8274 |
| 0.4 | 28407 | 5.3741 |
| 0.5 | 36284 | 6.8643 |
| 0.6 | 52209 | 9.8771 |
| 0.7 | 70135 | 13.2684 |
| 0.8 | 91425 | 17.2961 |
| 0.9 | 224216 | 42.4180 |
| 1.0 | 394 | 0.0745 |
| Total | 528587 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 331414 | 73.4976 |
| 0.1 | 30520 | 6.7684 |
| 0.2 | 23106 | 5.1242 |
| 0.3 | 15653 | 3.4714 |
| 0.4 | 13167 | 2.9200 |
| 0.5 | 11149 | 2.4725 |
| 0.6 | 8850 | 1.9627 |
| 0.7 | 8258 | 1.8314 |
| 0.8 | 5626 | 1.2477 |
| 0.9 | 3175 | 0.7041 |
| Total | 450918 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 23205 | 5.1462 |
| 0.4 | 26222 | 5.8152 |
| 0.5 | 35251 | 7.8176 |
| 0.6 | 47373 | 10.5059 |
| 0.7 | 59987 | 13.3033 |
| 0.8 | 75212 | 16.6798 |
| 0.9 | 183254 | 40.6402 |
| 1.0 | 414 | 0.0918 |
| Total | 450918 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 349865 | 72.9769 |
| 0.1 | 34517 | 7.1998 |
| 0.2 | 23288 | 4.8575 |
| 0.3 | 17634 | 3.6782 |
| 0.4 | 14136 | 2.9486 |
| 0.5 | 10703 | 2.2325 |
| 0.6 | 9768 | 2.0375 |
| 0.7 | 8042 | 1.6774 |
| 0.8 | 6556 | 1.3675 |
| 0.9 | 4910 | 1.0242 |
| Total | 479419 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 21188 | 4.4195 |
| 0.4 | 23890 | 4.9831 |
| 0.5 | 32012 | 6.6772 |
| 0.6 | 45178 | 9.4235 |
| 0.7 | 61083 | 12.7410 |
| 0.8 | 80331 | 16.7559 |
| 0.9 | 215268 | 44.9018 |
| 1.0 | 469 | 0.0978 |
| Total | 479419 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 268904 | 72.8196 |
| 0.1 | 29275 | 7.9277 |
| 0.2 | 18717 | 5.0686 |
| 0.3 | 13440 | 3.6396 |
| 0.4 | 9669 | 2.6184 |
| 0.5 | 8856 | 2.3982 |
| 0.6 | 6920 | 1.8739 |
| 0.7 | 6206 | 1.6806 |
| 0.8 | 4604 | 1.2468 |
| 0.9 | 2683 | 0.7266 |
| Total | 369274 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 19544 | 5.2925 |
| 0.4 | 23128 | 6.2631 |
| 0.5 | 28493 | 7.7160 |
| 0.6 | 38990 | 10.5586 |
| 0.7 | 48736 | 13.1978 |
| 0.8 | 61386 | 16.6234 |
| 0.9 | 148533 | 40.2230 |
| 1.0 | 464 | 0.1257 |
| Total | 369274 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 275018 | 73.3595 |
| 0.1 | 26906 | 7.1770 |
| 0.2 | 18262 | 4.8713 |
| 0.3 | 13518 | 3.6058 |
| 0.4 | 11255 | 3.0022 |
| 0.5 | 8610 | 2.2967 |
| 0.6 | 7984 | 2.1297 |
| 0.7 | 5790 | 1.5444 |
| 0.8 | 4643 | 1.2385 |
| 0.9 | 2905 | 0.7749 |
| Total | 374891 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 17139 | 4.5717 |
| 0.4 | 19556 | 5.2164 |
| 0.5 | 25659 | 6.8444 |
| 0.6 | 36383 | 9.7050 |
| 0.7 | 47916 | 12.7813 |
| 0.8 | 62547 | 16.6840 |
| 0.9 | 165402 | 44.1200 |
| 1.0 | 289 | 0.0771 |
| Total | 374891 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 164583 | 72.1441 |
| 0.1 | 15793 | 6.9228 |
| 0.2 | 10466 | 4.5877 |
| 0.3 | 9211 | 4.0376 |
| 0.4 | 7017 | 3.0759 |
| 0.5 | 6139 | 2.6910 |
| 0.6 | 4857 | 2.1290 |
| 0.7 | 4435 | 1.9441 |
| 0.8 | 3999 | 1.7529 |
| 0.9 | 1631 | 0.7149 |
| Total | 228131 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 11224 | 4.9200 |
| 0.4 | 12183 | 5.3404 |
| 0.5 | 15785 | 6.9193 |
| 0.6 | 22366 | 9.8040 |
| 0.7 | 28606 | 12.5393 |
| 0.8 | 37683 | 16.5181 |
| 0.9 | 100079 | 43.8691 |
| 1.0 | 205 | 0.0899 |
| Total | 228131 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 159777 | 73.1074 |
| 0.1 | 15525 | 7.1036 |
| 0.2 | 10987 | 5.0272 |
| 0.3 | 7860 | 3.5964 |
| 0.4 | 6734 | 3.0812 |
| 0.5 | 5084 | 2.3262 |
| 0.6 | 4487 | 2.0531 |
| 0.7 | 4002 | 1.8312 |
| 0.8 | 2644 | 1.2098 |
| 0.9 | 1451 | 0.6639 |
| Total | 218551 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 11663 | 5.3365 |
| 0.4 | 13065 | 5.9780 |
| 0.5 | 16314 | 7.4646 |
| 0.6 | 21998 | 10.0654 |
| 0.7 | 28113 | 12.8634 |
| 0.8 | 35011 | 16.0196 |
| 0.9 | 92228 | 42.1998 |
| 1.0 | 159 | 0.0728 |
| Total | 218551 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 383695 | 74.6310 |
| 0.1 | 33277 | 6.4726 |
| 0.2 | 23765 | 4.6224 |
| 0.3 | 17762 | 3.4548 |
| 0.4 | 14134 | 2.7491 |
| 0.5 | 11831 | 2.3012 |
| 0.6 | 10745 | 2.0900 |
| 0.7 | 9428 | 1.8338 |
| 0.8 | 5748 | 1.1180 |
| 0.9 | 3738 | 0.7271 |
| Total | 514123 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 32574 | 6.3358 |
| 0.4 | 36801 | 7.1580 |
| 0.5 | 45289 | 8.8090 |
| 0.6 | 56043 | 10.9007 |
| 0.7 | 66226 | 12.8814 |
| 0.8 | 80207 | 15.6007 |
| 0.9 | 195806 | 38.0854 |
| 1.0 | 1177 | 0.2289 |
| Total | 514123 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering